Create mosaïc

Different solutions to recreate mosaics of tiles of images from µManager, including correction of the illumination and camera field;

TODO

• Create 2 subprojects
  • ImageJ jython script (tested on macos)
  • Matlab scripts (external executable provided for macos)
• [ ]

Install

Necessary files

• Dark : series of dark images corresponding to your set of filters with their respective acquisition times, recorded in the dark without the beam.
• Bightfield: a Z stack of brightfields: lame matthieu without any filter
• Your stack of images to reconstruct
• For more info, look at the respective HowTo in the subfolders.

Known possible bugs

• During the acquisition process in µManager, if you did not check "Save in separate files" your stack of images will be saved in a single file impossible to reconstruct. In that case, you may open it again with µManager and "Save as separate files"
• Missing Metadata.

Reconstruct your mosaïc

Authors

• Marie-Françoise Devaux
• Fred JammeS
• Hugo Chauvet